Recent study shows that Apolipoprotein CIII (CIII) specifically binds and inhibits Lipoprotein Lipase (LpL) and Hepatic Lipase (HL) enzymes. The significance of the N-terminal domain in stabilizing the lipid-protein interaction and displacing Apolipoprotein E (E) was also identified (1). Our previous study that confirms the ability of CIII to displace E (2), sets up the stage for further structure-function studies evaluating the factors that enable CIII to displace E, and inhibits both HL and LpL. These functions should be investigated in correlation to CIIl's ability to bind to the lipoprotein particle (Lp) with varying size and composition. The cooperative and complex conformational modification of CIII binding to Lp and LpL/HL suggests that this study requires a factorial design experiment that can extract latent variable (factors) from collinear measurements of the protein's physico-chemical properties and structure (X-matrix), and relate these factors to the extracted latent variables from the Y-matrix consisting of the protein's functions. This study will be the first attempt to evaluate the structural factors in CIII that is responsible for the above functions in a systematic way using a factorial designed experiments. By using our model structure of CIII generated by homology with E crystal structure followed by molecular mechanics modeling, we are able to identify significant residues in CIII that may give us information regarding the difference in its function with respect to E and CII. Structural factors such as helix length, positive helix cap, loop flexibility, and hydrophobicity of side chains will be evaluated using different constructs in order to assess their contribution to the different functions of CIII. This approach is designed to give us a surface plot describing how the structural factors of CIII correlate with its functions. A more structured search and prediction of Clll analog that has a high lipid binding ability but with lipase inhibitory sites replaced by either the activating site of CII or E can be made using this approach.